Phylogenetic relationships of the great cats based on mitochondrial DNA sequence analysis

Nucleic acid sequence comparisons of three regions of the mitochondrial DNA (mtDNA) genome were used to elucidate the phylogenetic relationships of members of the Panthera lineage of the Felidae. PCR (polymerase chain reaction) was used to amplify 400-800 base pair segments from the 12S RNA gene (12S), cytochrome b protein coding region (Cytb) and the displacement loop (D-loop) for direct nucleic acid sequencing via dideoxy chain-termination reaction. Twenty-two species were analyzed including seventeen felids, one hyaenid, two canids and two ursids. Subspecies comparisons were made for five felid species. Sequences were computer aligned and the percent divergence was calculated for intra- and interspecific comparisons. Evolutionary trees were constructed using three different algorithms (PAUP, maximum likelihood and FITCH) and a majority rule phylogeny was determined for these and previously published molecular data. Results support the separation of three major lineages among felids: the South American group, domestic cat lineage and pantherine lineage, in agreement with classification determined by other molecular techniques. Results also support the classification of five member species of the genus Panthera as a separate lineage that also includes the clouded leopard, Neofelis nebulosa. Based upon this association, we proposed that the clouded leopard be included in this genus and named Panthera nebulosa. Within Panthera, the data suggest a more recent ancestor of lion, leopard and jaguar; the tiger appears to be the most distant. Outside of Panthera, the data support a recent association between the cheetah and puma; these two species then form a separate group within the pantherine lineage, together with the bobcat, lynxes and marbled cat. In addition to resolution of relationships of extant cats, DNA was extracted and analyzed from the extinct North American saber-toothed cat (Smilodon fatalis) for phylogenetic analysis. Results place the divergence of the within the extant cat lineage, prior to the divergence of the Panthera but subsequent to the radiation of modern-day cats.